RetrogeneDB ID: retro_ggor_1638

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 2a:60643227..60643466(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: LSM6
• Ensembl ID: ENSGGOG00000001310
• Aliases: None
• Description: None

Sequence

>retro_ggor_1638
ATGAACCTTTGGAAGCAAACCTCCAGTGCCTTCTTAAAGCATATCATCAGAAGACCAGTTGTGGTAAAATTAAATCCTGG
AGTGAATTATTGAGGGGACCTGGCTTGCCTGGATGACTGCTCGAATATAGCCCTGAGAAGGCAGAGGAATATATAAGTGG
ACAACCGAAGACTAAGTATGGGTATGCATTTGTCTGAGGAAACAATGTGTTGCACATCAGTACACAGGAGAGAAGGATG

Alignment

ORF - retro_ggor_1638 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.14 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSLRKQTPSDFLKQIIGRPVVVKLNSGVDYRGVLACLDGYMNIAL-EQTEEYVNGQLKNKYGDAFIRGNN
          M.L.KQT.S.FLK.II.RPVVVKLN.GV.Y.G.LACLD...NIAL.E..EEY..GQ.K.KYG.AF..GNN
Retrocopy MNLWKQTSSAFLKHIIRRPVVVKLNPGVNY*GDLACLDDCSNIAL<EKAEEYISGQPKTKYGYAFV*GNN

Parental  VLYISTQKRRM
          VL.ISTQ.RRM
Retrocopy VLHISTQERRM

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain_prefrontal_cortex	0.00 RPM	9.73 RPM
SRP007412_cerebellum	0.00 RPM	9.18 RPM
SRP007412_heart	0.00 RPM	3.03 RPM
SRP007412_kidney	0.00 RPM	7.40 RPM
SRP007412_liver	0.00 RPM	8.60 RPM
SRP007412_testis	0.10 RPM	13.57 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_1638 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1638 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2107
Pan troglodytes	retro_ptro_1545
Pongo abelii	retro_pabe_1994
Macaca mulatta	retro_mmul_991

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014060	1 retrocopy	retro_btau_861,
Cavia porcellus	ENSCPOG00000015389	1 retrocopy	retro_cpor_368,
Dasypus novemcinctus	ENSDNOG00000009322	5 retrocopies	retro_dnov_1118, retro_dnov_176, retro_dnov_2092, retro_dnov_301, retro_dnov_664,
Homo sapiens	ENSG00000164167	2 retrocopies	retro_hsap_1948, retro_hsap_2107,
Gorilla gorilla	ENSGGOG00000001127	2 retrocopies	retro_ggor_1549, retro_ggor_225,
Gorilla gorilla	ENSGGOG00000001310	2 retrocopies	retro_ggor_1417, retro_ggor_1638 ,
Myotis lucifugus	ENSMLUG00000026355	1 retrocopy	retro_mluc_1859,
Monodelphis domestica	ENSMODG00000000526	4 retrocopies	retro_mdom_1027, retro_mdom_1383, retro_mdom_1983, retro_mdom_621,
Nomascus leucogenys	ENSNLEG00000005584	2 retrocopies	retro_nleu_1275, retro_nleu_1479,
Otolemur garnettii	ENSOGAG00000026665	1 retrocopy	retro_ogar_233,
Sus scrofa	ENSSSCG00000009036	2 retrocopies	retro_sscr_474, retro_sscr_475,
Tarsius syrichta	ENSTSYG00000012759	4 retrocopies	retro_tsyr_1332, retro_tsyr_1727, retro_tsyr_340, retro_tsyr_653,